Multiple sequence alignment - TraesCS7D01G513900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G513900 chr7D 100.000 2951 0 0 1 2951 614796067 614793117 0.000000e+00 5450.0
1 TraesCS7D01G513900 chr7D 98.470 1895 29 0 94 1988 614729681 614727787 0.000000e+00 3339.0
2 TraesCS7D01G513900 chr7D 96.142 648 25 0 360 1007 614816232 614815585 0.000000e+00 1059.0
3 TraesCS7D01G513900 chr7D 95.330 364 17 0 1 364 614816642 614816279 1.970000e-161 579.0
4 TraesCS7D01G513900 chr7D 88.354 395 43 3 365 758 14414096 14414488 3.440000e-129 472.0
5 TraesCS7D01G513900 chr7D 86.351 359 49 0 6 364 14413686 14414044 2.760000e-105 392.0
6 TraesCS7D01G513900 chr7D 94.079 152 8 1 2043 2193 503337063 503337214 2.290000e-56 230.0
7 TraesCS7D01G513900 chr7D 95.172 145 7 0 2048 2192 552165960 552165816 2.290000e-56 230.0
8 TraesCS7D01G513900 chr7A 96.380 1630 55 2 784 2412 710803590 710805216 0.000000e+00 2680.0
9 TraesCS7D01G513900 chr7A 93.979 1229 45 7 824 2046 710503619 710502414 0.000000e+00 1832.0
10 TraesCS7D01G513900 chr7A 93.556 1226 50 7 824 2043 707800564 707801766 0.000000e+00 1799.0
11 TraesCS7D01G513900 chr7A 93.797 1193 62 5 790 1973 707545900 707544711 0.000000e+00 1783.0
12 TraesCS7D01G513900 chr7A 90.410 1220 76 12 778 1973 710480166 710478964 0.000000e+00 1567.0
13 TraesCS7D01G513900 chr7A 93.649 1055 50 8 941 1981 707497543 707496492 0.000000e+00 1561.0
14 TraesCS7D01G513900 chr7A 97.278 551 13 2 2402 2951 710806107 710806656 0.000000e+00 933.0
15 TraesCS7D01G513900 chr7A 95.467 375 15 2 2579 2951 707495436 707495062 5.440000e-167 597.0
16 TraesCS7D01G513900 chr7A 93.067 375 23 3 2579 2951 710499997 710499624 2.000000e-151 545.0
17 TraesCS7D01G513900 chr7A 92.267 375 26 3 2579 2951 707803747 707804120 2.010000e-146 529.0
18 TraesCS7D01G513900 chr7A 93.994 333 19 1 2067 2399 707496494 707496163 1.220000e-138 503.0
19 TraesCS7D01G513900 chr7A 94.444 126 6 1 2402 2527 195277315 195277439 3.000000e-45 193.0
20 TraesCS7D01G513900 chr7A 92.969 128 6 3 2408 2533 195278172 195278046 1.810000e-42 183.0
21 TraesCS7D01G513900 chr7A 91.071 56 3 2 2527 2582 566510848 566510795 1.130000e-09 75.0
22 TraesCS7D01G513900 chrUn 93.210 1193 69 5 790 1973 298697617 298696428 0.000000e+00 1744.0
23 TraesCS7D01G513900 chrUn 93.897 934 45 5 790 1714 427480078 427481008 0.000000e+00 1399.0
24 TraesCS7D01G513900 chrUn 93.399 409 25 2 360 767 81311460 81311053 3.250000e-169 604.0
25 TraesCS7D01G513900 chrUn 91.484 364 31 0 1 364 81311870 81311507 4.390000e-138 501.0
26 TraesCS7D01G513900 chrUn 93.694 333 20 1 2067 2399 298700075 298699744 5.680000e-137 497.0
27 TraesCS7D01G513900 chrUn 93.750 304 13 3 790 1087 384585456 384585759 4.490000e-123 451.0
28 TraesCS7D01G513900 chrUn 94.397 232 11 2 2579 2808 298699017 298698786 3.620000e-94 355.0
29 TraesCS7D01G513900 chrUn 95.238 126 4 2 2402 2527 67460735 67460612 6.450000e-47 198.0
30 TraesCS7D01G513900 chrUn 95.238 126 4 2 2402 2527 339772952 339772829 6.450000e-47 198.0
31 TraesCS7D01G513900 chrUn 93.750 64 4 0 2518 2581 252762147 252762210 2.420000e-16 97.1
32 TraesCS7D01G513900 chrUn 93.750 64 4 0 2518 2581 384721214 384721151 2.420000e-16 97.1
33 TraesCS7D01G513900 chrUn 92.982 57 4 0 2522 2578 67459897 67459841 1.880000e-12 84.2
34 TraesCS7D01G513900 chr6D 93.532 402 25 1 357 758 380504306 380504706 5.440000e-167 597.0
35 TraesCS7D01G513900 chr6D 90.934 364 33 0 1 364 380503899 380504262 9.500000e-135 490.0
36 TraesCS7D01G513900 chr6D 86.056 251 33 2 2698 2947 468860811 468861060 4.850000e-68 268.0
37 TraesCS7D01G513900 chr6D 93.671 158 8 2 2048 2203 256727864 256727707 4.920000e-58 235.0
38 TraesCS7D01G513900 chr6D 94.444 126 6 1 2402 2527 337505862 337505986 3.000000e-45 193.0
39 TraesCS7D01G513900 chr5D 93.048 374 26 0 360 733 311466552 311466179 5.560000e-152 547.0
40 TraesCS7D01G513900 chr5D 92.308 364 28 0 1 364 311466962 311466599 4.360000e-143 518.0
41 TraesCS7D01G513900 chr5D 92.308 364 28 0 1 364 533246832 533246469 4.360000e-143 518.0
42 TraesCS7D01G513900 chr5D 94.558 147 8 0 2048 2194 302355427 302355573 8.230000e-56 228.0
43 TraesCS7D01G513900 chr5D 93.750 64 4 0 2518 2581 4566555 4566618 2.420000e-16 97.1
44 TraesCS7D01G513900 chr5D 92.188 64 4 1 2518 2581 4487837 4487899 4.050000e-14 89.8
45 TraesCS7D01G513900 chr5D 96.226 53 2 0 2522 2574 4723043 4723095 1.460000e-13 87.9
46 TraesCS7D01G513900 chr2D 90.547 402 36 2 357 758 563782735 563783134 5.600000e-147 531.0
47 TraesCS7D01G513900 chr2D 91.086 359 32 0 6 364 563782333 563782691 1.230000e-133 486.0
48 TraesCS7D01G513900 chr2D 86.967 399 51 1 360 758 13140003 13139606 5.800000e-122 448.0
49 TraesCS7D01G513900 chr6A 87.562 402 49 1 357 758 91337864 91338264 5.760000e-127 464.0
50 TraesCS7D01G513900 chr6A 92.857 140 6 4 2395 2533 524714021 524713885 1.790000e-47 200.0
51 TraesCS7D01G513900 chr6A 95.238 126 5 1 2402 2527 524713122 524713246 6.450000e-47 198.0
52 TraesCS7D01G513900 chr6A 96.491 57 2 0 2522 2578 524713171 524713115 8.710000e-16 95.3
53 TraesCS7D01G513900 chr2A 83.791 401 58 7 360 758 655766040 655765645 9.990000e-100 374.0
54 TraesCS7D01G513900 chr2A 95.333 150 7 0 2048 2197 26861928 26861779 3.800000e-59 239.0
55 TraesCS7D01G513900 chr4A 82.682 358 60 2 8 364 688502006 688501650 1.710000e-82 316.0
56 TraesCS7D01G513900 chr4B 93.564 202 12 1 2212 2412 398088499 398088700 1.720000e-77 300.0
57 TraesCS7D01G513900 chr4B 92.118 203 15 1 2211 2412 465476252 465476454 4.810000e-73 285.0
58 TraesCS7D01G513900 chr4B 90.610 213 16 4 2202 2412 170675970 170675760 2.240000e-71 279.0
59 TraesCS7D01G513900 chr3D 93.596 203 10 3 2212 2412 62813600 62813801 1.720000e-77 300.0
60 TraesCS7D01G513900 chr3A 91.866 209 15 2 2205 2412 424088811 424089018 1.030000e-74 291.0
61 TraesCS7D01G513900 chr3A 82.576 132 21 2 2397 2527 734265028 734265158 6.680000e-22 115.0
62 TraesCS7D01G513900 chr1D 92.079 202 15 1 2212 2412 76970952 76971153 1.730000e-72 283.0
63 TraesCS7D01G513900 chr1D 95.862 145 6 0 2050 2194 480810618 480810762 4.920000e-58 235.0
64 TraesCS7D01G513900 chr2B 83.658 257 40 2 2696 2951 374506224 374505969 1.060000e-59 241.0
65 TraesCS7D01G513900 chr4D 94.737 133 5 2 2402 2533 157975957 157976088 3.860000e-49 206.0
66 TraesCS7D01G513900 chr6B 95.238 126 5 1 2402 2527 188503088 188502964 6.450000e-47 198.0
67 TraesCS7D01G513900 chr1B 96.552 58 2 0 2522 2579 175274375 175274318 2.420000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G513900 chr7D 614793117 614796067 2950 True 5450.000000 5450 100.0000 1 2951 1 chr7D.!!$R3 2950
1 TraesCS7D01G513900 chr7D 614727787 614729681 1894 True 3339.000000 3339 98.4700 94 1988 1 chr7D.!!$R2 1894
2 TraesCS7D01G513900 chr7D 614815585 614816642 1057 True 819.000000 1059 95.7360 1 1007 2 chr7D.!!$R4 1006
3 TraesCS7D01G513900 chr7D 14413686 14414488 802 False 432.000000 472 87.3525 6 758 2 chr7D.!!$F2 752
4 TraesCS7D01G513900 chr7A 710803590 710806656 3066 False 1806.500000 2680 96.8290 784 2951 2 chr7A.!!$F3 2167
5 TraesCS7D01G513900 chr7A 707544711 707545900 1189 True 1783.000000 1783 93.7970 790 1973 1 chr7A.!!$R3 1183
6 TraesCS7D01G513900 chr7A 710478964 710480166 1202 True 1567.000000 1567 90.4100 778 1973 1 chr7A.!!$R4 1195
7 TraesCS7D01G513900 chr7A 710499624 710503619 3995 True 1188.500000 1832 93.5230 824 2951 2 chr7A.!!$R6 2127
8 TraesCS7D01G513900 chr7A 707800564 707804120 3556 False 1164.000000 1799 92.9115 824 2951 2 chr7A.!!$F2 2127
9 TraesCS7D01G513900 chr7A 707495062 707497543 2481 True 887.000000 1561 94.3700 941 2951 3 chr7A.!!$R5 2010
10 TraesCS7D01G513900 chrUn 427480078 427481008 930 False 1399.000000 1399 93.8970 790 1714 1 chrUn.!!$F3 924
11 TraesCS7D01G513900 chrUn 298696428 298700075 3647 True 865.333333 1744 93.7670 790 2808 3 chrUn.!!$R5 2018
12 TraesCS7D01G513900 chrUn 81311053 81311870 817 True 552.500000 604 92.4415 1 767 2 chrUn.!!$R4 766
13 TraesCS7D01G513900 chr6D 380503899 380504706 807 False 543.500000 597 92.2330 1 758 2 chr6D.!!$F3 757
14 TraesCS7D01G513900 chr5D 311466179 311466962 783 True 532.500000 547 92.6780 1 733 2 chr5D.!!$R2 732
15 TraesCS7D01G513900 chr2D 563782333 563783134 801 False 508.500000 531 90.8165 6 758 2 chr2D.!!$F1 752

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
30 31 1.004927 CGGTGATTTTCGATTCTCCGC 60.005 52.381 16.05 1.02 40.68 5.54 F
841 2511 1.012086 CAAGGACGTGATCATGCCAG 58.988 55.000 22.41 14.32 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 3449 0.741221 GTGCGTCATCTTCTGGGACC 60.741 60.0 0.0 0.0 0.0 4.46 R
2141 3856 0.392193 CAGCACCACACTCCATCTCC 60.392 60.0 0.0 0.0 0.0 3.71 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.004927 CGGTGATTTTCGATTCTCCGC 60.005 52.381 16.05 1.02 40.68 5.54
702 805 1.447217 CATGCCGCTGGGTCAGATA 59.553 57.895 0.00 0.00 32.44 1.98
841 2511 1.012086 CAAGGACGTGATCATGCCAG 58.988 55.000 22.41 14.32 0.00 4.85
1322 3029 4.322801 CCAAGAAGAGGACCGTTTCTACAT 60.323 45.833 12.21 0.00 31.30 2.29
1324 3031 3.833070 AGAAGAGGACCGTTTCTACATGT 59.167 43.478 2.69 2.69 29.82 3.21
1928 3638 1.203287 TGAATCAGTGCTCACTCCTCG 59.797 52.381 0.00 0.00 40.20 4.63
2133 3848 4.323417 TCTGTACATTGGCGTCTTGAATT 58.677 39.130 0.00 0.00 0.00 2.17
2141 3856 1.133025 GGCGTCTTGAATTGATGGTGG 59.867 52.381 0.00 0.00 0.00 4.61
2154 3869 0.914644 ATGGTGGGAGATGGAGTGTG 59.085 55.000 0.00 0.00 0.00 3.82
2165 3880 2.363306 TGGAGTGTGGTGCTGAAATT 57.637 45.000 0.00 0.00 0.00 1.82
2194 3909 6.095021 AGTGAATGTCGTCTGTATAGCAGTTA 59.905 38.462 0.00 0.00 45.23 2.24
2225 3940 8.433421 TCTTTGTGATTTACTCTCTTCGTTTT 57.567 30.769 0.00 0.00 0.00 2.43
2477 6858 7.283625 TGTGTTATTTGCAAAACTATGACCT 57.716 32.000 17.19 0.00 0.00 3.85
2547 6928 5.472137 GGCCATATAGTTTCCGAATTTGCTA 59.528 40.000 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.087771 ATCGAAAATCACCGTCGGCC 61.088 55.000 12.28 0.0 35.51 6.13
345 346 0.718408 AAAGGATGCCCCCATTTCCT 59.282 50.000 0.00 0.0 34.66 3.36
841 2511 2.298729 CCTATGGAGTCCTAGAGCAAGC 59.701 54.545 11.33 0.0 0.00 4.01
1322 3029 1.561717 GCGCACGTACATGGTCAACA 61.562 55.000 0.30 0.0 0.00 3.33
1324 3031 1.288419 CTGCGCACGTACATGGTCAA 61.288 55.000 5.66 0.0 0.00 3.18
1739 3449 0.741221 GTGCGTCATCTTCTGGGACC 60.741 60.000 0.00 0.0 0.00 4.46
1928 3638 2.713770 CATGCATGGCGCTGAGTC 59.286 61.111 19.40 0.0 43.06 3.36
2133 3848 1.206878 CACTCCATCTCCCACCATCA 58.793 55.000 0.00 0.0 0.00 3.07
2141 3856 0.392193 CAGCACCACACTCCATCTCC 60.392 60.000 0.00 0.0 0.00 3.71
2165 3880 4.783764 ATACAGACGACATTCACTGACA 57.216 40.909 0.00 0.0 34.88 3.58
2194 3909 9.651913 GAAGAGAGTAAATCACAAAGAGAAGAT 57.348 33.333 0.00 0.0 0.00 2.40
2225 3940 9.914834 ACCAAACCTTATATGCAGACTAATAAA 57.085 29.630 0.00 0.0 0.00 1.40
2228 3943 7.573710 TGACCAAACCTTATATGCAGACTAAT 58.426 34.615 0.00 0.0 0.00 1.73
2575 6956 3.498661 GGTTGAAGGTGAAGGACTTGGAT 60.499 47.826 0.00 0.0 0.00 3.41
2911 7294 2.435372 ACACCAATGGCGGATACATT 57.565 45.000 0.00 0.0 39.00 2.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.